vcf2pcadapt uses the package vcfR to extract the genotype information from a vcf file and exports it under the format required by pcadapt. Note that this VCF converter is not maintained anymore. Please use PLINK.

vcf2pcadapt(input, output = "tmp.pcadapt", allele.sep = c("/", "|"))

Arguments

input

a character string specifying the name of the file to be converted.

output

a character string indicating the name of the output file.

allele.sep

a vector of characters indicating what delimiters are used to separate alleles.